feat: add suggest command and harden citation resolution#41
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Add the candidate-only `suggest` command plus a batch of correctness fixes, and scope Google Scholar to `suggest` only. Features: - `onecite suggest`: return candidate matches for plain-text references without producing authoritative BibTeX. `process` now resolves only strong identifiers (DOI/PMID/arXiv/ISBN/URL) and points plain text to `suggest`. - Stable JSON/NDJSON envelopes for process/suggest, plus `doctor`, `benchmark`, and `templates` commands; CrossRef polite-pool headers; reuse of input BibTeX citation keys. Fixes: - DOI-backed BibTeX keeps canonical CrossRef/DataCite fields instead of the original entry's values (original still fills gaps; key preserved). - CrossRef 404 always falls back to DataCite (was limited to ~11 hardcoded prefixes). - `suggest` thesis routing uses whole-word matching (no longer fires on "synthesis"/"hypothesis"/"parenthesis"). - GitHub clone URLs ending in `.git` resolve to the correct repository. - Plain-text entry ids stay contiguous; removed a dead PLOS branch. Changes: - Google Scholar is now an opt-in, best-effort fallback on `suggest` only; removed `--google-scholar` from `process` and the `use_google_scholar` parameter from `process_references()` (both were no-ops there). Documented as not guaranteed reproducible. Tests: 191 passed, 1 skipped; flake8 clean on onecite + tests.
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Summary
suggestcommand: returns candidate matches forplain-text references without producing authoritative BibTeX.
processnowresolves only strong identifiers (DOI/PMID/arXiv/ISBN/URL) and points plain
text to
suggest.process/suggest, plusdoctor,benchmark, andtemplatescommands; CrossRef polite-pool headers; reuse ofinput BibTeX citation keys.
suggestonly — an opt-in, best-effort fallback(off by default, may be CAPTCHA-blocked, not guaranteed reproducible).
Removed
--google-scholarfromprocessand theuse_google_scholarparameter from
process_references()(both were no-ops there).Fixes
original entry's values (original still fills gaps; citation key preserved).
prefixes).
suggestthesis routing uses whole-word matching (no longer fires on"synthesis"/"hypothesis"/"parenthesis").
.gitresolve to the correct repository.dead PLOS article-id branch in the text parser.
Test plan
pytest: 191 passed, 1 skipped, 6 deselected (live-marked).flake8 onecite tests: clean.onecite process --helpno longer shows--google-scholar;onecite suggest --helpstill does.